Tandem Repeats Finder Program written by:

                 Gary Benson
      Program in Bioinformatics
          Boston University

Version 4.09

Sequence: Scaffold3203

Parameters: 2 7 7 80 10 50 1000

Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000

Length: 13060
ACGTcount: A:0.36, C:0.10, G:0.18, T:0.35


Found at i:3236 original size:28 final size:28

Alignment explanation


    Indices: 3183--3266  Score: 132
    Period size: 28  Copynumber: 3.0  Consensus size: 28

       3173 CACTTTGTGC

                                         
       3183 TATTCTGGTGTGTTTTGGATGGATTATAT
          1 TATTCTGGTGTGTTTTGGA-GGATTATAT

                           *            
       3212 TATTCTGGTGTGTTTGGGAGGATTATAT
          1 TATTCTGGTGTGTTTTGGAGGATTATAT

            *  *                       
       3240 GATACTGGTGTGTTTTGGAGGATTATA
          1 TATTCTGGTGTGTTTTGGAGGATTATA

       3267 CTGGTGTGTT


Statistics
Matches: 51,  Mismatches: 4, Indels: 1
        0.91            0.07        0.02

Matches are distributed among these distances:
  28   33  0.65
  29   18  0.35

ACGTcount: A:0.19, C:0.04, G:0.31, T:0.46


Consensus pattern (28 bp):   
TATTCTGGTGTGTTTTGGAGGATTATAT

Found at i:3278 original size:23 final size:24

Alignment explanation


    Indices: 3187--3280  Score: 91
    Period size: 28  Copynumber: 3.6  Consensus size: 24

       3177 TTGTGCTATT

                                       
       3187 CTGGTGTGTTTTGGATGGATTATATTA
          1 CTGGTGTGTTTTGGA-GGA-TATA-TA

                         *                
       3214 TTCTGGTGTGTTTGGGAGGATTATATGATA
          1 --CTGGTGTGTTTTGGAGG---ATAT-ATA

                                    
       3244 CTGGTGTGTTTTGGAGGAT-TATA
          1 CTGGTGTGTTTTGGAGGATATATA

                          
       3267 CTGGTGTGTTTTGG
          1 CTGGTGTGTTTTGG

       3281 TTGGACATTT


Statistics
Matches: 59,  Mismatches: 2, Indels: 14
        0.79            0.03        0.19

Matches are distributed among these distances:
  23   17  0.29
  24    1  0.02
  25    2  0.03
  28   18  0.31
  29   14  0.24
  30    5  0.08
  31    2  0.03

ACGTcount: A:0.16, C:0.04, G:0.34, T:0.46


Consensus pattern (24 bp):   
CTGGTGTGTTTTGGAGGATATATA

Found at i:3508 original size:22 final size:23

Alignment explanation


    Indices: 3471--3515  Score: 83
    Period size: 22  Copynumber: 2.0  Consensus size: 23

       3461 GCTTTACTGA

                                   
       3471 TCAGGCACTTTATGTGTCGTATT
          1 TCAGGCACTTTATGTGTCGTATT

                                   
       3494 TCAGGCAC-TTATGTGTCGTATT
          1 TCAGGCACTTTATGTGTCGTATT

       3516 CTGATCAGGT


Statistics
Matches: 22,  Mismatches: 0, Indels: 1
        0.96            0.00        0.04

Matches are distributed among these distances:
  22   14  0.64
  23    8  0.36

ACGTcount: A:0.18, C:0.18, G:0.22, T:0.42


Consensus pattern (23 bp):   
TCAGGCACTTTATGTGTCGTATT

Found at i:8947 original size:33 final size:32

Alignment explanation


    Indices: 8900--8962  Score: 92
    Period size: 33  Copynumber: 1.9  Consensus size: 32

       8890 ACAATTGTAA

                     *                       
       8900 TATTTTATTTAAATT-AGTAGATATTTATTATT
          1 TATTTTATTAAAATTAAG-AGATATTTATTATT

                                           
       8932 TATTATTATTAAAATTAAGAGATATTTATTA
          1 TATT-TTATTAAAATTAAGAGATATTTATTA

       8963 ATTAAATAAT


Statistics
Matches: 28,  Mismatches: 1, Indels: 3
        0.88            0.03        0.09

Matches are distributed among these distances:
  32    4  0.14
  33   22  0.79
  34    2  0.07

ACGTcount: A:0.40, C:0.00, G:0.06, T:0.54


Consensus pattern (32 bp):   
TATTTTATTAAAATTAAGAGATATTTATTATT

Found at i:8984 original size:33 final size:33

Alignment explanation


    Indices: 8904--8984  Score: 87
    Period size: 33  Copynumber: 2.5  Consensus size: 33

       8894 TTGTAATATT

                 *                       *  * 
       8904 TTATTTAAATT-AGTAGATATTTATTATTTATTA
          1 TTATTAAAATTAAG-AGATATTTATTATTAATAA

                                               
       8937 TTATTAAAATTAAGAGATATTTATTAATTAAATAA
          1 TTATTAAAATTAAGAGATATTTATT-ATT-AATAA

                           
       8972 TTA-TAAAA-TAAGA
          1 TTATTAAAATTAAGA

       8985 TTTTTATGTG


Statistics
Matches: 42,  Mismatches: 3, Indels: 6
        0.82            0.06        0.12

Matches are distributed among these distances:
  33   26  0.62
  34   10  0.24
  35    6  0.14

ACGTcount: A:0.47, C:0.00, G:0.06, T:0.47


Consensus pattern (33 bp):   
TTATTAAAATTAAGAGATATTTATTATTAATAA

Found at i:9549 original size:23 final size:23

Alignment explanation


    Indices: 9519--9563  Score: 65
    Period size: 23  Copynumber: 2.0  Consensus size: 23

       9509 GTGAATTAAA

                                   
       9519 ATTGATTGAAAA-GTGAAAAATG
          1 ATTGATTGAAAATGTGAAAAATG

                              *    
       9541 ATTGAATTGAAAATGTGAGAAAT
          1 ATTG-ATTGAAAATGTGAAAAAT

       9564 TGTGACTGAA


Statistics
Matches: 20,  Mismatches: 1, Indels: 2
        0.87            0.04        0.09

Matches are distributed among these distances:
  22    4  0.20
  23    8  0.40
  24    8  0.40

ACGTcount: A:0.49, C:0.00, G:0.22, T:0.29


Consensus pattern (23 bp):   
ATTGATTGAAAATGTGAAAAATG

Done.